The airport, which is one of the world's busiest, has been the site of daily protests since Friday.
Videos on social media showed passengers struggling to get through demonstrators, who were sitting inside and blocking departures.
Amid tense scenes, police and protesters clashed outside the airport.
The police, wearing riot gear and brandishing truncheons, are said to have deployed pepper spray to push protesters back.
In an ugly incident, young protesters mobbed a man they suspected was an undercover policeman and zip-tied his hands together. Paramedics struggled to treat the man amid a crowd of angry protesters before he was taken to hospital.
The editor of China's Global Times newspaper said the man was one of his reporters who was merely doing his job.
Hong Kong police have admitted deploying officers disguised as anti-government protesters during the unrest in the city.
The city's leader, Carrie Lam, earlier issued a fresh warning to protesters.
Ms Lam said Hong Kong had "reached [a] dangerous situation" and that violence during protests would push it "down a path of no return".
Meanwhile, Chinese state media have published images of convoys of military police gathering in the border city of Shenzhen, says the BBC's Stephen McDonell, who is in Hong Kong.
US President Donald Trump said on Twitter that US intelligence had informed him of a deployment by "troops", adding: "Everyone should be calm and safe."
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